Attempts by the health secretary Andy Burnham to strengthen the NHS's hand in the face of competition from the private healthcare sector face a serious challenge, after a government advisory body announced it would be investigating the effects of the policy.

In what amounts to a non-legal "class action", the government's competition commission has agreed to look at a complaint brought by hundreds of charities and private sector companies angered by a decision, made by the health secretary in September, that the NHS would be the "preferred provider" of NHS care.

This means failing or underperforming NHS trusts would be allowed to keep an NHS contract to allow them to improve, rather than allowing charities and private companies a chance to take over provision of that service.

Burnham's decision surprised cabinet colleagues and industry insiders alike, as it appeared to renege on a Labour 2005 manifesto pledge that the voluntary and community sector "should be considered on equal terms" as the NHS, and contradicted the efforts of other members of the cabinet who had in recent months been calling for an increased role for charities and non-state actors in the provision of public services.

The unexpected development in Labour health policy was seen as a sop to the unions – increasingly important in bankrolling the general election campaign. But government advisers insist the health secretary's embrace of the "preferred provider" phrase was more a measure to rally the NHS troops and that any shift in public policy was inadvertent.

At the end of December, the NHS Partners Network – which represents private providers of NHS care – and Acevo, the Association of Chief Executives of Voluntary Organisations, put in a joint complaint to the NHS's Co-operation and Competition Panel which today has been accepted.

Their case rests on a decision by an east of England primary care trust (PCT) to exclude them from bidding to provide NHS services, which they claim breaches NHS rules and guidance on competition and choice.

Great Yarmouth and Waveney PCT originally invited NHS organisations, the private sector and voluntary organisations to bid to run its community health services but after Burnham's speech in September declaring that NHS organisations were now the "preferred provider" of NHS care, the PCT blocked bids from the private and voluntary sectors ,saying it would now "only be able to accept bids from NHS organisations".

The charities and private providers believe the investigation being launched today provides them with a chance for redress, but the prospects are uncertain. Burnham's new direction in health policy has not yet received official cabinet approval and once it has done so, their chances of the competition commission finding in their favour will diminish.

However if the commission does find in their favour, they believe Burnham may be forced to review his decision, and modify his position to see patients still able to be treated by the best organisation of NHS, charity or private on merit.

Peter Kyle, the deputy chair of ACEVO, said: "Although this is a complaint against one PCT, it is the first instance of a PCT implementing Andy Burnham's 'preferred provider' policy, so can therefore be interpreted as a complaint against the secretary of state's position.

The real significance of this on a public policy and political level is that the official guidance to commissioners on 'preferred provider' policy is due for clearance soon, and [the Department of Health] is also trying to alter the remit of the competition panel.

Both would need cabinet sign-off, at which time it will become official government policy. We would therefore not be able to bring this complaint in the future.

So I have a unique opportunity here to have Andy Burnham's future policy judged by today's standards and it is highly possible they will say that it is anti-competitive.

This would mean that an independent NHS panel set up by the previous health secretary could in effect rule that [Burnham] is rolling back on competitive practice and failing to act in the best interests of patients and tax payers."